Origin of genes

Nucleotide-level distance metrics to quantify alternative splicing implemented in TranD

Advances in affordable transcriptome sequencing combined with better exon and gene prediction has motivated many to compare transcription across the tree of life. We develop a mathematical framework to calculate complexity and compare transcript models. Structural features, i.e. intron retention (IR), donor/acceptor site variation, alternative exon cassettes, alternative 5'/3' UTRs, are compared and the distance between transcript models is calculated with nucleotide level precision. All metrics are implemented in a PyPi package, TranD and output can be used to summarize splicing patterns for a transcriptome (1GTF) and between transcriptomes (2GTF). TranD output enables quantitative comparisons between: annotations augmented by empirical RNA-seq data and the original transcript models; transcript model prediction tools for longread RNA-seq (e.g. FLAIR versus Isoseq3); alternate annotations for a species (e.g. RefSeq vs Ensembl); and between closely related species. In C. elegans, Z. mays, D. melanogaster, D. simulans and H. sapiens, alternative exons were observed more frequently in combination with an alternative donor/acceptor than alone. Transcript models in RefSeq and Ensembl are linked and both have unique transcript models with empirical support. D. melanogaster and D. simulans, share many transcript models and long-read RNAseq data suggests that both species are under-annotated. We recommend combined references.

Genome-Wide Identification and Expression Analysis under Abiotic Stress of BrAHL Genes in Brassica rapa

The AT-hook motif nuclear localized (AHL) gene family is a highly conserved transcription factor critical for the growth, development, and stress tolerance of plants. However, the function of the AHL gene family in Brassica rapa (B. rapa) remains unclear. In this study, 42 AHL family members were identified from the B. rapa genome and mapped to nine B. rapa chromosomes. Two clades have formed in the evolution of the AHL gene family. The results showed that most products encoded by AHL family genes are located in the nucleus. Gene duplication was common and expanded the BrAHL gene family. According to the analysis of cis-regulatory elements, the genes interact with stress responses (osmotic, cold, and heavy metal stress), major hormones (abscisic acid), and light responses. In addition, the expression profiles revealed that BrAHL genes are widely expressed in different tissues. BrAHL16 was upregulated at 4 h under drought stress, highly expressed under cadmium conditions, and downregulated in response to cold conditions. BrAHL02 and BrAHL24 were upregulated at the initial time point and peaked at 12 h under cold and cadmium stress, respectively. Notably, the interactions between AHL genes and proteins under drought, cold, and heavy metal stresses were observed when predicting the protein-protein interaction network.

Genetic portrait of polyamine transporters in barley: insights in the regulation of leaf senescence

Nitrogen (N) is one of the most expensive nutrients to supply, therefore, improving the efficiency of N use is essential to reduce the cost of commercial fertilization in plant production. Since cells cannot store reduced N as NH₃ or NH₄ ⁺, polyamines (PAs), the low molecular weight aliphatic nitrogenous bases, are important N storage compounds in plants. Manipulating polyamines may provide a method to increase nitrogen remobilization efficiency. Homeostasis of PAs is maintained by intricate multiple feedback mechanisms at the level of biosynthesis, catabolism, efflux, and uptake. The molecular characterization of the PA uptake transporter (PUT) in most crop plants remains largely unknown, and knowledge of polyamine exporters in plants is lacking. Bi-directional amino acid transporters (BATs) have been recently suggested as possible PAs exporters for Arabidopsis and rice, however, detailed characterization of these genes in crops is missing. This report describes the first systematic study to comprehensively analyze PA transporters in barley (Hordeum vulgare, Hv), specifically the PUT and BAT gene families. Here, seven PUTs (HvPUT1-7) and six BATs (HvBAT1-6) genes were identified as PA transporters in the barley genome and the detailed characterization of these HvPUT and HvBAT genes and proteins is provided. Homology modeling of all studied PA transporters provided 3D structures prediction of the proteins of interest with high accuracy. Moreover, molecular docking studies provided insights into the PA-binding pockets of HvPUTs and HvBATs facilitating improved understanding of the mechanisms and interactions involved in HvPUT/HvBAT-mediated transport of PAs. We also examined the physiochemical characteristics of PA transporters and discuss the function of PA transporters in barley development, and how they help barley respond to stress, with a particular emphasis on leaf senescence. Insights gained here could lead to improved barley production via modulation of polyamine homeostasis.

Genome-wide identification of DnaJ gene family in Catalpa bungei and functional analysis of CbuDnaJ49 in leaf color formation

DnaJs are the common molecular chaperone proteins with strong structural and functional diversity. In recent years, only several DnaJ family members have been found to be able to regulate leaf color, and it remains to be explored whether there are other potential members that also regulate this character. Here, we identified 88 putative DnaJ proteins from Catalpa bungei, and classified them into four types according to their domain. Gene-structure analysis revealed that each member of CbuDnaJ family had same or similar exon-intron structure. Chromosome mapping and collinearity analysis showed that tandem and fragment duplication occurred in the process of evolution. Promoter analyses suggested that CbuDnaJs might be involved in a variety of biological processes. The expression levels of DnaJ family members in different color leaves of Maiyuanjinqiu were respectively extracted from the differential transcriptome. Among these, CbuDnaJ49 was the largest differentially expressed gene between the green and yellow sectors. Ectopic overexpression of CbuDnaJ49 in tobacco showed that the positive transgenic seedlings exhibited albino leaves, and the contents of chlorophyll and carotenoid were significantly reduced compared with those of wild type. The results suggested that CbuDnaJ49 played an important role in regulating leaf color. This study not only identified a novel gene of DnaJ family members regulating leaf color, but also provided new germplasm for landscaping.

Phylogenetic, structural, functional characterisation and effect of exogenous spermidine on rice (Oryza sativa) HAK transporters under salt stress

The HAK (High-affinity K+ ) family members mediate K+ transport that confers normal plant growth and resistance against unfavourable environmental conditions. Rice (Oryza sativa L.) HAK transporters have been extensively investigated for phylogenetic analyses with other plants species with very few of them functionally characterised. But very little information is known about their evolutionary aspects, overall structural, functional characterisation, and global expression pattern of the complete HAK family members in response to salt stress. In this study, 27 rice transporters were phylogenetically clustered with different dicot and monocot family members. Subsequently, the exon-intron structural patterns, conserved motif analyses, evolutionary divergence based different substitution matrix, orthologous-paralogous relationships were studied elaborately. Structural characterisations included a comparative study of secondary and tertiary structure, post-translational modifications, correspondence analyses, normal mode analyses, K+ /Na+ binding affinities of each of the OsHAK gene members. Global expression profile under salt stress showed clade-specific expression pattern of the proteins. Additionally, five OsHAK genes were chosen for further expression analyses in root and shoot tissues of two rice varieties during short-term salinity in the presence and absence of exogenous spermidine. All the information can be used as first-hand data for dissecting the administrative role of rice HAK transporters under various abiotic stresses.

Reconstruction of human genome evolution in yeast: an educational primer for use with "systematic humanization of the yeast cytoskeleton discerns functionally replaceable from divergent human genes"

The evolution of eukaryotic organisms starting with the last eukaryotic common ancestor was accompanied by lineage-specific expansion of gene families. A paper by Garge et al. provides an excellent opportunity to have students explore how expansion of gene families via gene duplication results in protein specialization, in this case in the context of eukaryotic cytoskeletal organization . The authors tested hypotheses about conserved protein function by systematic "humanization" of the yeast cytoskeletal components while employing a wide variety of methodological approaches. We outline several exercises to promote students' ability to explore the genomic databases, perform bioinformatic analyses, design experiments for functional analysis of human genes in yeast and critically interpret results to address both specific and general questions.

Processed pseudogenes: A substrate for evolutionary innovation: Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome

Processed pseudogenes may serve as a genetic reservoir for evolutionary innovation. Here, we argue that through the activity of long interspersed element-1 retrotransposons, processed pseudogenes disperse coding and noncoding sequences rich with regulatory potential throughout the human genome. While these sequences may appear to be non-functional, a lack of contemporary function does not prohibit future development of biological activity. Here, we discuss the dynamic evolution of certain processed pseudogenes into coding and noncoding genes and regulatory elements, and their implication in wide-ranging biological and pathological processes. Also see the video abstract here: https://youtu.be/iUY_mteVoPI.

Spliceosomal Introns: Features, Functions, and Evolution

Spliceosomal introns, which have been found in most eukaryotic genes, are non-coding sequences excised from pre-mRNAs by a special complex called spliceosome during mRNA splicing. Introns occur in both protein- and RNA-coding genes and can be found in coding and untranslated gene regions. Because intron sequences vary greatly due to a high rate of polymorphism, the functions of intron had been for a long time associated only with alternative splicing, while intron evolution had been viewed not as an evolution of an individual genomic element, but rather considered within a framework of the evolution of the gene intron-exon structure. Here, we review the theories of intron origin, evolutionary events in the exon-intron structure, such as intron gain, loss, and sliding, intron functions known to date, and mechanisms by which changes in the intron features (length and phase) can affect the regulation of gene-mediated processes.

The Chloroplast Trans-Splicing RNA-Protein Supercomplex from the Green Alga Chlamydomonas reinhardtii

In eukaryotes, RNA trans-splicing is a significant RNA modification process for the end-to-end ligation of exons from separately transcribed primary transcripts to generate mature mRNA. So far, three different categories of RNA trans-splicing have been found in organisms within a diverse range. Here, we review trans-splicing of discontinuous group II introns, which occurs in chloroplasts and mitochondria of lower eukaryotes and plants. We discuss the origin of intronic sequences and the evolutionary relationship between chloroplast ribonucleoprotein complexes and the nuclear spliceosome. Finally, we focus on the ribonucleoprotein supercomplex involved in trans-splicing of chloroplast group II introns from the green alga Chlamydomonas reinhardtii. This complex has been well characterized genetically and biochemically, resulting in a detailed picture of the chloroplast ribonucleoprotein supercomplex. This information contributes substantially to our understanding of the function of RNA-processing machineries and might provide a blueprint for other splicing complexes involved in trans- as well as cis-splicing of organellar intron RNAs.

Genome-Wide Identification and Expression Analysis of the Class III Peroxidase Gene Family in Potato (Solanum tuberosum L.)

Class III peroxidases (PRXs) are plant-specific enzymes and play important roles in plant growth, development and stress response. In this study, a total of 102 non-redundant PRX gene members (StPRXs) were identified in potato (Solanum tuberosum L.). They were divided into 9 subfamilies based on phylogenetic analysis. The members of each subfamily were found to contain similar organizations of the exon/intron structures and protein motifs. The StPRX genes were not equally distributed among chromosomes. There were 57 gene pairs of segmental duplication and 26 gene pairs of tandem duplication. Expression pattern analysis based on the RNA-seq data of potato from public databases indicated that StPRX genes were expressed differently in various tissues and responded specifically to heat, salt and drought stresses. Most of the StPRX genes were expressed at significantly higher levels in root than in other tissues. In addition, real-time quantitative PCR (qRT-PCR) analysis for 7 selected StPRX genes indicated that these genes displayed various expression levels under abiotic stresses. Our results provide valuable information for better understanding the evolution of StPRX gene family in potato and lay the vital foundation for further exploration of PRX gene function in plants.

Genome-wide identification of the class III POD gene family and their expression profiling in grapevine (Vitis vinifera L)

BACKGROUND

The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress tolerance. The POD family members have been well-studied and characterized by bioinformatics analysis in several plant species, but no previous genome-wide analysis has been carried out of this gene family in grapevine to date.

RESULTS

We comprehensively identified 47 PODs in the grapevine genome and are further classified into 7 subgroups based on their phylogenetic analysis. Results of motif composition and gene structure organization analysis revealed that PODs in the same subgroup shared similar conjunction while the protein sequences were highly conserved. Intriguingly, the integrated analysis of chromosomal mapping and gene collinearity analysis proposed that both dispersed and tandem duplication events contributed to the expansion of PODs in grapevine. Also, the gene duplication analysis suggested that most of the genes (20) were dispersed followed by (15) tandem, (9) segmental or whole-genome duplication, and (3) proximal, respectively. The evolutionary analysis of PODs, such as Ka/Ks ratio of the 15 duplicated gene pairs were less than 1.00, indicated that most of the gene pairs exhibiting purifying selection and 7 pairs underwent positive selection with value greater than 1.00. The Gene Ontology Enrichment (GO), Kyoto Encyclopedia of Genes Genomics (KEGG) analysis, and cis-elements prediction also revealed the positive functions of PODs in plant growth and developmental activities, and response to stress stimuli. Further, based on the publically available RNA-sequence data, the expression patterns of PODs in tissue-specific response during several developmental stages revealed diverged expression patterns. Subsequently, 30 genes were selected for RT-PCR validation in response to (NaCl, drought, and ABA), which showed their critical role in grapevine.

CONCLUSIONS

In conclusion, we predict that these results will lead to novel insights regarding genetic improvement of grapevine.

Design of novel protein building modules and modular architectures

Nature uses only a limited number of protein topologies and while several folds have evolved independently over time, there are clearly many possible topologies that have not been explored by evolution. With recent advances of protein design concepts, computational modeling tools, high resolution and high-throughput experimental methods it is now possible to design new protein architectures. The collection of building blocks and design principles widened both in size and complexity, offering an expanded toolset for building new modular folds and functional protein structures. Here we review and discuss recent achievements of protein design, focusing in particular on the use and prospects of modular approaches for assembling new protein folds.

Evolution of the genetic code based on conservative changes of codons, amino acids, and aminoacyl tRNA synthetases

The genetic code, as arranged in the standard tabular form, displays a non-random structure relating to the characteristics of the amino acids. An alternative arrangement can be made by organizing the code according to aminoacyl-tRNA synthetases (aaRSs), codons, and reverse complement codons, which illuminates a coevolutionary process that led to the contemporary genetic code. As amino acids were added to the genetic code, they were recognized by aaRSs that interact with stereochemically similar amino acids. Single nucleotide changes in the codons and anticodons were favored over more extensive changes, such that there was a logical stepwise progression in the evolution of the genetic code. The model presented traces the evolution of the genetic code accounting for these steps. Amino acid frequencies in ancient proteins and the preponderance of GNN codons in mRNAs for ancient proteins indicate that the genetic code began with alanine, aspartate, glutamate, glycine, and valine, with alanine being in the highest proportions. In addition to being consistent in terms of conservative changes in codon nucleotides, the model also is consistent with respect to aaRS classes, aaRS attachment to the tRNA, amino acid stereochemistry, and to a large extent with amino acid physicochemistry, and biochemical pathways.

Integrated evolution of ribosomal RNAs, introns, and intron nurseries

The initial components of ribosomes first appeared more than 3.8 billion years ago during a time when many types of RNAs were evolving. While modern ribosomes are complex molecular machines consisting of rRNAs and proteins, they were assembled during early evolution by the association and joining of small functional RNA units. Introns may have provided the means to ligate many of these pieces together. All four classes of introns (group I, group II, spliceosomal, and archaeal) are present in many rRNA gene loci over a broad phylogenetic range. A survey of rRNA intron sequences across the three major life domains suggests that some of the classes of introns may have diverged from one another within rRNA gene loci. Analyses of rRNA sequences revealed self-splicing group I and group II introns are present in ancestral regions of the SSU (small subunit) and LSU (large subunit), whereas spliceosomal and archaeal introns appeared in sections of the rRNA that evolved later. Most classes of introns increased in number for approximately 1 billion years. However, their frequencies are low in the most recently evolved regions added to the SSU and LSU rRNAs. Furthermore, many of the introns appear to have been in the same locations for billions of years, suggesting an ancient origin for these sequences. In this Perspectives paper, I reviewed and analyzed rRNA intron sequences, locations, structural characteristics, and splicing mechanisms; and suggest that rRNA gene loci may have served as evolutionary nurseries for intron formation and diversification.

Pseudogene-derived lncRNAs: emerging regulators of gene expression

In the more than one decade since the completion of the Human Genome Project, the prevalence of non-protein-coding functional elements in the human genome has emerged as a key revelation in post-genomic biology. Highlighted by the ENCODE (Encyclopedia of DNA Elements) and FANTOM (Functional Annotation of Mammals) consortia, these elements include tens of thousands of pseudogenes, as well as comparably numerous long non-coding RNA (lncRNA) genes. Pseudogene transcription and function remain insufficiently understood. However, the field is of great importance for human disease due to the high sequence similarity between pseudogenes and their parental protein-coding genes, which generates the potential for sequence-specific regulation. Recent case studies have established essential and coordinated roles of both pseudogenes and lncRNAs in development and disease in metazoan systems, including functional impacts of lncRNA transcription at pseudogene loci on the regulation of the pseudogenes’ parental genes. This review synthesizes the nascent evidence for regulatory modalities jointly exerted by lncRNAs and pseudogenes in human disease, and for recent evolutionary origins of these systems.

Peculiaritats al·lèliques del locus <em>S</em> de les cultivars mallorquines d’ametller

El examen de la diversidad alélica del locus S en diez cultivares mallorquines de almendro ha mostrado la presencia del alelo Sf en cuatro de ellos, así como la presencia de cinco nuevos alelos no identificados hasta ahora. Aunque el alelo Sf se ha descrito como responsable de la expresión de la autocompatibilidad del almendro, recientemente se ha descubierto que tiene dos expresiones fenotípicas diferentes, por lo que no siempre se puede considerar un índice de la autocompatibilidad de los genotipos que lo presentan. El estudio de los cuatro cultivares mallorquines que presentan este alelo ha confirmado su autoincompatibilidad, de manera que este alelo se expresa en estos cultivares en su forma fenotípicamente activa, como también se ha comprobado en un grupo de cultivares del sur de Italia, lo que podría indicar una conexión entre estas dos poblaciones mediterráneas de almendro. [ca] L’examen de la diversitat al·lèlica del locus S en deu cultivars mallorquines d’ametller ha mostrat la presència de l’al·lel Sf en quatre, així com la presència de cinc al·lels nous fins ara no identificats. Encara que l’al·lel Sf s’ha descrit com a responsable de l’expressió de l’autocompatibilitat de l’ametller, fa poc que s’ha descobert que té dues expressions fenotípiques diferents, pel que no sempre es pot considerar un índex de l’autocompatibilitat dels genotips que el tenen. L’estudi de les quatre cultivars mallorquines que presenten aquest al·lel ha confirmat la seva autoincompatibilitat, de manera que aquest al·lel s’hi expressa en la seva forma fenotípicament activa, com també s’ha comprovat en un grup de cultivars del sud d’Itàlia, fet que podria indicar una connexió entre aquestes dues poblacions mediterrànies d’ametller.

Genome-wide analysis and evolutionary study of sucrose non-fermenting 1-related protein kinase 2 (SnRK2) gene family members in Arabidopsis and Oryza

The over-expression of plant specific SnRK2 gene family members by hyperosmotic stress and some by abscisic acid is well established. In this report, we have analyzed the evolution of SnRK2 gene family in different plant lineages including green algae, moss, lycophyte, dicot and monocot. Our results provide some evidences to indicate that the natural selection pressure had considerable influence on cis-regulatory promoter region and coding region of SnRK2 members in Arabidopsis and Oryza independently through time. Observed degree of sequence/motif conservation amongst SnRK2 homolog in all the analyzed plant lineages strongly supported their inclusion as members of this family. The chromosomal distributions of duplicated SnRK2 members have also been analyzed in Arabidopsis and Oryza. Massively Parallel Signature Sequencing (MPSS) database derived expression data and the presence of abiotic stress related promoter elements within the 1 kb upstream promoter region of these SnRK2 family members further strengthen the observations of previous workers. Additionally, the phylogenetic relationships of SnRK2 have been studied in all plant lineages along with their respective exon-intron structural patterns. Our results indicate that the ancestral SnRK2 gene of land plants gradually evolved by duplication and diversification and modified itself through exon-intron loss events to survive under environmental stress conditions.

Alternative splice variants in TIM barrel proteins from human genome correlate with the structural and evolutionary modularity of this versatile protein fold

After the surprisingly low number of genes identified in the human genome, alternative splicing emerged as a major mechanism to generate protein diversity in higher eukaryotes. However, it is still not known if its prevalence along the genome evolution has contributed to the overall functional protein diversity or if it simply reflects splicing noise. The (βα)₈ barrel or TIM barrel is one of the most frequent, versatile, and ancient fold encountered among enzymes. Here, we analyze the structural modifications present in TIM barrel proteins from the human genome product of alternative splicing events. We found that 87% of all splicing events involved deletions; most of these events resulted in protein fragments that corresponded to the (βα)₂, (βα)₄, (βα)₅, (βα)₆, and (βα)₇ subdomains of TIM barrels. Because approximately 7% of all the splicing events involved internal β-strand substitutions, we decided, based on the genomic data, to design β-strand and α-helix substitutions in a well-studied TIM barrel enzyme. The biochemical characterization of one of the chimeric variants suggests that some of the splice variants in the human genome with β-strand substitutions may be evolving novel functions via either the oligomeric state or substrate specificity. We provide results of how the splice variants represent subdomains that correlate with the independently folding and evolving structural units previously reported. This work is the first to observe a link between the structural features of the barrel and a recurrent genetic mechanism. Our results suggest that it is reasonable to expect that a sizeable fraction of splice variants found in the human genome represent structurally viable functional proteins. Our data provide additional support for the hypothesis of the origin of the TIM barrel fold through the assembly of smaller subdomains. We suggest a model of how nature explores new proteins through alternative splicing as a mechanism to diversify the proteins encoded in the human genome.

Pseudogenes

Pseudogenes are ubiquitous and abundant in genomes. Pseudogenes were once called “genomic fossils” and treated as “junk DNA” several years. Nevertheless, it has been recognized that some pseudogenes play essential roles in gene regulation of their parent genes, and many pseudogenes are transcribed into RNA. Pseudogene transcripts may also form small interfering RNA or decrease cellular miRNA concentration. Thus, pseudogenes regulate tumor suppressors and oncogenes. Their essential functions draw the attention of our research group in my current work on heat shock protein 90: a chaperone of oncogenes. The paper reviews our current knowledge on pseudogenes and evaluates preliminary results of the chaperone data. Current efforts to understand pseudogenes interactions help to understand the functions of a genome.

Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life

This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution-leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.

The construction of "phylomer" peptide libraries as a rich source of potent inhibitors of protein/protein interactions

Phylomer libraries are made from random overlapping genome fragments of biodiverse bacteria and Archaea. They provide a rich source of high-affinity binders to protein interfaces, and can be used both for target-directed screening approaches and for phenotypic screens to discover new targets. Here, we describe methods used for the construction of a Phylomer library, illustrated by examples of construction in both a yeast two-hybrid vector and a phage display vector.

Theory of the origin, evolution, and nature of life

Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations. The theoretical framework unifies the macrocosmic and microcosmic realms, validates predicted laws of nature, and solves the puzzle of the origin and evolution of cellular life in the universe.

Phenotypic screening of phylomer peptide libraries derived from genome fragments to identify and validate new targets and therapeutics

BACKGROUND

Phenotypic screening of random peptide libraries has been hampered by very poor hit rates. This is probably due to the fact that random combinatorial peptide libraries contain an insufficiently large proportion of secondary and/or tertiary structures that are likely to interact in a stable manner with multiple classes of potential target proteins. Phylomer libraries, by contrast, are derived from sequences of genomes that have been through millions to billions of years of evolution and were therefore hypothesized to be more likely to encode appropriate structures, which have been selected to stably bind with high affinity to protein surfaces. This approach is analogous to small-molecule libraries constructed to provide a rich source of structures (often found in natural products) that are common to the pharmacophores of known drugs.

DISCUSSION

Phenotypic screens of phylomer libraries show very high hit rates for bioactive peptides, suggesting that they may be a useful tool for target discovery and validation. Biophysical evidence suggests that this high activity may be due to the high proportion of affinities of unmodified peptides in the low nanomolar range.

CONCLUSION

The high hit rates from phylomer libraries are sufficient to allow libraries composed of synthetic peptides to be synthesized and screened in parallel high-throughput screening formats. In addition to allowing the identification of new targets, the phylomer peptides themselves may be useful as structural probes to map epitopes of target vulnerability and as leads in therapeutic discovery.

Premature transcript termination, trans-splicing and DNA repair: a vicious path to cancer

So far, about 800 different chromosomal translocations have been characterized in hemato-malignant and solid tumors. Chromosomal translocations mostly result in the expression of chimeric fusion proteins associated with enhanced proliferation and/or malignant transformation. Here, we demonstrate that genes frequently involved in such genetic rearrangements exhibit a unique feature: premature transcriptional termination. These early-terminated RNA molecules have an abundance of 10-20% when compared to their cognate full-length transcripts. They exhibit an unsaturated splice donor site that gives rise to trans-splicing events, leading to RNAs displaying exon repetitions or chimeric fusion RNAs. These arbitrary fusion RNAs mimic the presence of a chromosomal translocation in genetically unaffected cells. Based on our and published data, we propose the hypothesis that these artificial "chimeric fusion transcripts" may influence DNA repair processes, resulting in the generation of de novo chromosomal translocations. This idea provides a rational explanation why different individuals suffer from nearly identical genetic rearrangements.

Information-theoretic model of evolution over protein communication channel

In this paper, we propose a communication model of evolution and investigate its information-theoretic bounds. The process of evolution is modeled as the retransmission of information over a protein communication channel, where the transmitted message is the organism's proteome encoded in the DNA. We compute the capacity and the rate distortion functions of the protein communication system for the three domains of life: Archaea, Bacteria, and Eukaryotes. The tradeoff between the transmission rate and the distortion in noisy protein communication channels is analyzed. As expected, comparison between the optimal transmission rate and the channel capacity indicates that the biological fidelity does not reach the Shannon optimal distortion. However, the relationship between the channel capacity and rate distortion achieved for different biological domains provides tremendous insight into the dynamics of the evolutionary processes of the three domains of life. We rely on these results to provide a model of genome sequence evolution based on the two major evolutionary driving forces: mutations and unequal crossovers.

Evolution of galanin receptor genes: insights from the deuterostome genomes

Galanin exerts its biological activities through three different G protein-coupled receptors, Galr1, Galr2 and Galr3. To obtain insights into the evolution of Galrs, we searched the genomes of the deuterostomes by extensive BLAST survey and phylogenetic analyses. The Galr2 and Galr3 share similar genomic structures, and most of them are composed of 2 exons and 1 intron. However, most of Galr1 are composed of 3 extrons and 2 introns. We did not detect the typical Galr genes in the genomic databases of invertebrate deutserotomes, but three Galr1/Alstr homologs and two Galr1/Gpr151 homologs in amphioxus, two Galr1/Gpr151 homologs in sea squirt and one Galr1/Gpr151 homologs in sea urchin were identified. It is highly possible that the Galr genes in vertebrates may evolve from the homologous genes of Galr1/Alstr/Gpr151 in invertebrate deuterostomes. We also proposed that Galr3 genes were the products of Galr2 duplication during evolution, while Galr2 genes may evolve from Galr1.

Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication

BACKGROUND

Positions of spliceosomal introns are often conserved between remotely related genes. Introns that reside in non-conserved positions are either novel or remnants of frequent losses of introns in some evolutionary lineages. A recent gain of such introns is difficult to prove. However, introns verified as novel are needed to evaluate contemporary processes of intron gain.

RESULTS

We identified 25 unambiguous cases of novel intron positions in 31 Drosophila genes that exhibit near intron pairs (NIPs). Here, a NIP consists of an ancient and a novel intron position that are separated by less than 32 nt. Within a single gene, such closely-spaced introns are very unlikely to have coexisted. In most cases, therefore, the ancient intron position must have disappeared in favour of the novel one. A survey for NIPs among 12 Drosophila genomes identifies intron sliding (migration) as one of the more frequent causes of novel intron positions. Other novel introns seem to have been gained by regional tandem duplications of coding sequences containing a proto-splice site.

CONCLUSIONS

Recent intron gains sometimes appear to have arisen by duplication of exonic sequences and subsequent intronization of one of the copies. Intron migration and exon duplication together may account for a significant amount of novel intron positions in conserved coding sequences.

Evolutionary insights into insecticide resistance gene families of Anopheles gambiae

Insecticide resistance (IR) is one of the major obstacles in insect pests and insect borne disease control strategies, the mechanism of which is known to be genetically controlled. Three major gene families (CYP, GST and COE) have been identified encoding various proteins to metabolize endogenous as well as exogenous compounds that are responsible for IR mechanisms in insects. Understanding evolutionary patterns of genes of such important functions could lead to important understanding, based on which, further studies to control various insect borne infectious diseases could be initiated. We herein utilized the whole genome sequence information of the malaria vector Anopheles gambiae and inferred evolutionary pattern of the three known IR gene families (CYP, GST and COE). The pattern of conservation of IR genes across 38 other taxa was determined to infer evolutionary pattern of these gene families. Chromosomal distribution of IR genes was ascertained and each individual gene of IR gene families was also mapped on the chromosomal arms of An. gambiae. Differential distributional and quantitative aspects of introns in each gene were determined and genetic architecture of genes from all three gene families was compared to draw differential evolution of IR gene families. Further, phylogenetic relationships among genes of each of the three gene families were also inferred. These results in correlation with chromosomal location of each gene have provided valuable information about evolutionary history of IR gene families.

Analyzing S-adenosylhomocysteine hydrolase gene sequences in deuterostome genomes

S-adenosylhomocysteine hydrolase (SAHH) gene sequences of sea-urchin, two amphioxus, sea-squirt and eight vertebrates are comparatively analyzed in the current analysis. Although SAHH protein sequences are highly conserved in these species, their nucleotide sequences are much different, ranging from 5,446 bp in amphioxus to 40,174 bp in zebra fish. The length divergence is mainly caused by distinct introns in some species. SAHH genes in amphioxus (or sea-urchin), sea-squirt and vertebrates are composed of eight, nine and ten exons, respectively. Sequence alignment shows that exon 3 in amphioxus and sea-urchin is similar to exons 3 + 4 in vertebrates, exon 5 in amphioxus and sea-urchin is similar to exons 5 + 6 in sea-squirt, and the two exons are fused into exon 6 in vertebrates. Furthermore, exon 7 in sea-squirt is similar to exons 7 + 8 in vertebrates, indicating that exon-fission and exon-fusion events have been taken place during the evolution of deuterostome SAHH genes. Active sites and NAD+-binding sites are located in exons 2 7 in amphioxus, which are dispersed into much more exons along with the evolution of vertebrates. It is speculated that ten-exon organization of SAHH gene occurred after the separation of invertebrates and vertebrates. Synonymous and non-synonymous substitution analysis shows that negative selection plays a dominant role in the evolution of SAHH genes. Phylogenetic analysis shows that SAHH genes in amphioxus, sea-urchin and sea-squirt form a cluster and locate at the base of neighbor-joining tree, suggesting that they are the archetype of vertebrate SAHH genes.

Evolutionary genetic insights into Plasmodium falciparum functional genes

Complex and rapidly evolving behavior of the human malaria parasite Plasmodium falciparum have always been mysterious to the evolutionary biologists, as the parasite is the most virulent and now becoming the most prevalent malaria parasite species across the globe. With the availability of complete genome sequence of P. falciparum, better understanding of the genome design and evolution could be possible. We herein utilized the available information of all known functional genes from whole genome of P. falciparum and investigate the differential mode of gene evolution. The study comparing P. falciparum functional genes with Plasmodium vivax revealed about 82% of genes to be conserved in the later species and the rest, 18% to be totally unique to P. falciparum. Genetic architectural pattern of functional genes shows absence of introns in about a half of the conserved genes, whereas almost all unique genes have introns. Similarly, distribution of intron number and length were also observed to be different for conserved and unique genes of P. falciparum. Statistically significant positive correlations between total intron length and gene lengths were detected in 11 chromosomes for unique genes, whereas only in three chromosomes for conserved genes. Preference of intron presence in some P. falciparum genes were also detected which provide functional relevance of introns. The study provides, for the first time, a detail evolutionary analysis of functional genes of a devastating malaria parasite. The marked differences in organization of introns between the unique and conserved genes in P. falciparum, and the contribution of introns to genome complexity are some of the hallmarks of the study.

Intron-dominated genomes of early ancestors of eukaryotes

Evolutionary reconstructions using maximum likelihood methods point to unexpectedly high densities of introns in protein-coding genes of ancestral eukaryotic forms including the last common ancestor of all extant eukaryotes. Combined with the evidence of the origin of spliceosomal introns from invading Group II self-splicing introns, these results suggest that early ancestral eukaryotic genomes consisted of up to 80% sequences derived from Group II introns, a much greater contribution of introns than that seen in any extant genome. An organism with such an unusual genome architecture could survive only under conditions of a severe population bottleneck.

A chimaeric glutamyl:glutaminyl-tRNA synthetase: implications for evolution

aaRSs (aminoacyl-tRNA synthetases) are multi-domain proteins that have evolved by domain acquisition. The anti-codon binding domain was added to the more ancient catalytic domain during aaRS evolution. Unlike in eukaryotes, the anti-codon binding domains of GluRS (glutamyl-tRNA synthetase) and GlnRS (glutaminyl-tRNA synthetase) in bacteria are structurally distinct. This originates from the unique evolutionary history of GlnRSs. Starting from the catalytic domain, eukaryotic GluRS evolved by acquiring the archaea/eukaryote-specific anti-codon binding domain after branching away from the eubacteria family. Subsequently, eukaryotic GlnRS evolved from GluRS by gene duplication and horizontally transferred to bacteria. In order to study the properties of the putative ancestral GluRS in eukaryotes, formed immediately after acquiring the anti-codon binding domain, we have designed and constructed a chimaeric protein, cGluGlnRS, consisting of the catalytic domain, Ec GluRS (Escherichia coli GluRS), and the anti-codon binding domain of EcGlnRS (E. coli GlnRS). In contrast to the isolated EcN-GluRS, cGluGlnRS showed detectable activity of glutamylation of E. coli tRNAglu and was capable of complementing an E. coli ts (temperature-sensitive)-GluRS strain at non-permissive temperatures. Both cGluGlnRS and EcN-GluRS were found to bind E. coli tRNAglu with native EcGluRS-like affinity, suggesting that the anticodon-binding domain in cGluGlnRS enhances kcat for glutamylation. This was further confirmed from similar experiments with a chimaera between EcN-GluRS and the substrate-binding domain of EcDnaK (E. coli DnaK). We also show that an extended loop, present in the anticodon-binding domains of GlnRSs, is absent in archaeal GluRS, suggesting that the loop was a later addition, generating additional anti-codon discrimination capability in GlnRS as it evolved from GluRS in eukaryotes.

[Analysis of correlation of local GC level in human protein coding genes]

GC level is an important feature of genomic composition, which significantly improve our understanding of structure, function and evolution of genes. In this paper, the nonredundant DNA sequence of 7,992 human protein coding genes were retrieved from public database and the local GC level of different sequence regions and correlation between GC levels were analyzed.. The results showed that the GC levels of different sequence regions were strikingly nonuniform. 5' untranslated regions were of richest GC, with average GC content being 62.5%. 3'-untranslated regions were of poorest GC, with average GC content being 43.97%. GC contents of 3' flanking sequences profoundly matched the GC levels of DNA large fragments where the genes were located. Although the GC contents of open reading frames (ORFs) were higher than that of intron, 3' non-translated region and 3' flanking sequences, high correlation existed among the GC contents of the four regions. Average GC content of the third codon position (GC3) was 58.9%, higher than that of the fist and second position, and showed high correlation to GC contents of ORFs, with correlation coefficients being 0.91, besides of its significant association with GC contents of intron, 3'-untranslated region and 3' flanking sequences. Moreover, the linear regression of GC3 against GC contents of 3' flanking sequences yielded a slope of 1.25. Thus, GC3 was a sensitive indicator for GC change of local genome. As for 5' flanking sequences, 5' untranslated regions, fist and second codon position, however, their GC level exhibited weaker correlation with that of other regions. These results suggest that the third codon positions, introns, 3'-untranslated regions and 3' flanking sequences may evolve similarly while first and second codon positions, 5' flanking sequences and 5' untranslated region were expected to bear more selective stress for holding their functions.

Alternative splicing: a missing piece in the puzzle of intron gain

Spliceosomal introns, a hallmark of eukaryotic gene organization, were an unexpected discovery. After three decades, crucial issues such as when and how introns first appeared in evolution remain unsettled. An issue yet to be answered is how intron positions arise de novo. Phylogenetic investigations concur that intron positions continue to emerge, at least in some lineages. Yet genomic scans for the sources of introns occupying new positions have been fruitless. Two alternative solutions to this paradox are: (i) formation of new intron positions halted before the recent past and (ii) it continues to occur, but through processes different from those generally assumed. One process generally dismissed is intron sliding--the relocation of a preexisting intron over short distances--because of supposed associated deleterious effects. The puzzle of intron gain arises owing to a pervasive operational definition of introns, which sees them as precisely demarcated segments of the genome separated from the neighboring nonintronic DNA by unmovable limits. Intron homology is defined as position homology. Recent studies of pre-mRNA processing indicate that this assumption needs to be revised. We incorporate recent advances on the evolutionarily frequent process of alternative splicing, by which exons of primary transcripts are spliced in different patterns, into a new model of intron sliding that accounts for the diversity of intron positions. We posit that intron positional diversity is driven by two overlapping processes: (i) background process of continuous relocation of preexisting introns by sliding and (ii) spurts of extensive gain/loss of new intron sequences.

Duplication and functional diversification of HAP3 genes leading to the origin of the seed-developmental regulatory gene, LEAFY COTYLEDON1 (LEC1), in nonseed plant genomes

The HAP3 gene encodes a subunit of the CCAAT-box-binding factor (CBF), a highly conserved trimeric activator that recognizes and binds the ubiquitous CCAAT promoter element with high affinity. Two types of HAP3 gene have been identified in plant genomes. The LEAFY COTYLEDON1 (LEC1)-type HAP3 genes encode a functionally specialized subunit of CBF, which is expressed specifically in developing seeds. In contrast, most non-LEC1-type HAP3 genes are expressed in various tissues. It has been proposed that the LEC1-type HAP3 genes originated from the duplication and functional divergence of non-LEC1-type HAP3 genes. However, it is not yet known when this duplication event took place or whether the LEC1-type HAP3 genes appeared at the same time as the origin of seed plants. Here we describe a comprehensive comparison of the duplication patterns of HAP3 genes in different plant genomes. We recognize a major expansion of the HAP3 gene family accompanying the origin and early diversification of land plants and postulate that retrotransposition and other mechanisms of gene duplication have been involved in the expansion of the plant HAP3 gene family. We provide evidence that the LEC1-type HAP3 genes originated in nonseed vascular plant genomes and demonstrate that they are inductively expressed under drought stress in nonseed plants. These genes, however, were recruited to a novel regulatory network in the early stages of seed plant evolution and steadily expressed during seed development and maturation.

Recombination and population mosaic of a multifunctional viral gene, adeno-associated virus cap

Homologous recombination is a dominant force in evolution and results in genetic mosaics. To detect evidence of recombination events and assess the biological significance of genetic mosaics, genome sequences for various viral populations of reasonably large size are now available in the GenBank. We studied a multi-functional viral gene, the adeno-associated virus (AAV) cap gene, which codes for three capsid proteins, VP1, VP2 and VP3. VP1-3 share a common C-terminal domain corresponding to VP3, which forms the viral core structure, while the VP1 unique N-terminal part contains an enzymatic domain with phospholipase A2 activity. Our recombinant detection program (RecI) revealed five novel recombination events, four of which have their cross-over points in the N-terminal, VP1 and VP2 unique region. Comparison of phylogenetic trees for different cap gene regions confirmed discordant phylogenies for the recombinant sequences. Furthermore, differences in the phylogenetic tree structures for the VP1 unique (VP1u) region and the rest of cap highlighted the mosaic nature of cap gene in the AAV population: two dominant forms of VP1u sequences were identified and these forms are linked to diverse sequences in the rest of cap gene. This observation together with the finding of frequent recombination in the VP1 and 2 unique regions suggests that this region is a recombination hot spot. Recombination events in this region preserve protein blocks of distinctive functions and contribute to convergence in VP1u and divergence of the rest of cap. Additionally the possible biological significance of two dominant VP1u forms is inferred.

Selecting folded proteins from a library of secondary structural elements

A protein evolution strategy is described by which double-stranded DNA fragments encoding defined Escherichia coli protein secondary structural elements (alpha-helices, beta-strands, and loops) are assembled semirandomly into sequences comprised of as many as 800 amino acid residues. A library of novel polypeptides generated from this system was inserted into an enhanced green fluorescent protein (EGFP) fusion vector. Library members were screened by fluorescence activated cell sorting (FACS) to identify those polypeptides that fold into soluble, stable structures in vivo that comprised a subset of shorter sequences ( approximately 60 to 100 residues) from the semirandom sequence library. Approximately 108 clones were screened by FACS, a set of 1149 high fluorescence colonies were characterized by dPCR, and four soluble clones with varying amounts of secondary structure were identified. One of these is highly homologous to a domain of aspartate racemase from a marine bacterium (Polaromonas sp.) but is not homologous to any E. coli protein sequence. Several other selected polypeptides have no global sequence homology to any known protein but show significant alpha-helical content, limited dispersion in 1D nuclear magnetic resonance spectra, pH sensitive ANS binding and reversible folding into soluble structures. These results demonstrate that this strategy can generate novel polypeptide sequences containing secondary structure.

Ancient intron insertion sites and palindromic genomic duplication evolutionally shapes an elementally functioning membrane protein family

Background

In spite of the recent accumulation of genomic data, the evolutionary pathway in the individual genes of present-day living taxa is still elusive for most genes. Among ion channels, inward K⁺ rectifier (IRK) channels are the fundamental and well-defined protein group. We analyzed the genomic structures of this group and compared them among a phylogenetically wide range with our sequenced Halocynthia roretzi, a tunicate, IRK genomic genes.

Results

A total of 131 IRK genomic genes were analyzed. The phylogenic trees of amino acid sequences revealed a clear diversification of deuterostomic IRKs from protostomic IRKs and suggested that the tunicate IRKs are possibly representatives of the descendants of ancestor forms of three major groups of IRKs in the vertebrate. However, the exon-intron structures of the tunicate IRK genomes showed considerable similarities to those of Caenorhabditis. In the vertebrate clade, the members in each major group increased at least four times those in the tunicate by various types of global gene duplication. The generation of some major groups was inferred to be due to anti-tandem (palindromic) duplication in early history. The intron insertion points greatly decreased during the evolution of the vertebrates, remaining as a unique conservation of an intron insertion site in the portion of protein-protein interaction within the coding regions of all vertebrate G-protein-activated IRK genes.

Conclusion

From the genomic survey of a family of IRK genes, it was suggested that the ancient intron insertion sites and the unique palindromic genomic duplication evolutionally shaped this membrane protein family.

The tree of life might be rooted in the branch leading to Nanoarchaeota

It is suggested that the tree of life might be rooted in the domain of the Archaea, in the branch leading to the phylum of Nanoarchaeota. This hypothesis seems to be corroborated by the uniqueness and ancestrality of some traits possessed by Nanoarchaeum equitans, such as split genes separately codifying for the 5' and 3' halves of the tRNA molecule. These half genes are the oldest ancestral form of gene we have ever seen. This, along with the absence of operons from the genome of N. equitans, would seem to indicate that this genome is a molecular fossil of the evolutionary stage which the ancestral genomes had reached when the first lines of divergence were established. Moreover, the late appearance of DNA coinciding with the rooting of the universal phylogenetic tree would make the genome of N. equitans a witness to this fundamental event.